Moderate alkali de-esterification can change the physicochemical characteristics and thus the functional properties of high methoxyl pectin (HMP). The results revealed that de-esterification could increase negative charges (Zeta potential from −21 to −31 mV), decrease molecular weight (from 448 to 136 kDa) and apparent viscosity of HMP. Homogalacturonan (HG) content decreased (from 62% to 49%) while rhamnogalacturonan Ⅰ (RG-Ⅰ) content increased (from 32% to 46%) after de-esterification. The group characteristics of HMP with different degree of esterification (DE) were similar and no obvious impact was made on degree of crystallinity by alkali de-esterification. A conformation transition of HMP molecule implied by Congo red test were occurred as the DE decreased. With the decrease of DE, the molecular structure of HMP became shorter and smaller, and the entanglement was weaker. The de-esterification caused slight decrease of thermal stability. Alkali de-esterification would weaken the gel property and the emulsifying ability of HMP.